Estimate COI using naive allele-count methods

For every specimen, counts distinct alleles at each locus and sorts those counts in decreasing order. With method = "integer_method", the integer_threshold-th value is the COI estimate. With method = "quantile_method", the value at quantile_threshold is used instead (scaling naturally with the number of observed allele rows).

Usage

estimate_coi_naive(
  allele_table,
  output = NULL,
  method = "integer_method",
  integer_threshold = 1,
  quantile_threshold = 0.05
)

Arguments

allele_table

Path to an allele table TSV. See Inputs.

output

Optional output TSV path.

method

One of "integer_method" or "quantile_method". Default: "integer_method".

integer_threshold

Positive integer index into the ordered allele counts (integer method only). Default: 1.

quantile_threshold

Quantile in [0, 1] (quantile method only). Values near zero yield higher COI estimates. Default: 0.05.

Value

A tibble with columns specimen_name and coi.

Details

Inputs

• allele_table: Allele table (specimen_name, target_name, seq, reads). See vignette("input-formats", package = "PGEcore").

Outputs

• output (optional): COI table TSV with columns specimen_name and coi. If NULL, results are returned without writing a file.

Running

estimate_coi_naive(
  allele_table = "allele_table.tsv",
  output = "coi_table.tsv"
)

Rscript exec/estimate_coi_naive \
  --allele_table allele_table.tsv \
  --output coi_table.tsv

See also

vignette("input-formats", package = "PGEcore")

Examples

allele_path <- system.file(
  "extdata", "example_allele_table.tsv",
  package = "PGEcore"
)
estimate_coi_naive(allele_path, method = "integer_method")
#> # A tibble: 5 × 2
#>   specimen_name                                                              coi
#>   <chr>                                                                    <int>
#> 1 PARAV3-ENV-MH04-7S1-7C1-1000-parasitedensity-sampleDB-4064911117_S43_L0…     3
#> 2 PARAV3-ENV-MH04-DS2-DC11-1000-parasitedensity-sampleDB-4064911661_S35_L…     2
#> 3 PARAV3-ENV-MH04-DS2-DC11-10000-parasitedensity-sampleDB-4064911565_S30_…     3
#> 4 PARAV3-ENV-MH04-DS2-DC3-1000-parasitedensity-sampleDB-4064911200_S31_L0…     3
#> 5 PARAV3-ENV-MH04-DS4-DC2-1000-parasitedensity-sampleDB-4064911921_S14_L0…     3